Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora

Background Evolutionary patterns of scleractinian (stony) corals are difficult to infer given the existence of few diagnostic characters and pervasive phenotypic plasticity. A previous study of Hawaiian Montipora (Scleractinia: Acroporidae) based on five partial mitochondrial and two nuclear genes revealed the existence of a species complex, grouping one of the rarest known species (M. dilatata, which is listed as Endangered by the International Union for Conservation of Nature - IUCN) with widespread corals of very different colony growth forms (M. flabellata and M. cf. turgescens). These previous results could result from a lack of resolution due to a limited number of markers, compositional heterogeneity or reflect biological processes such as incomplete lineage sorting (ILS) or introgression. Results All 13 mitochondrial protein-coding genes from 55 scleractinians (14 lineages from this study) were used to evaluate if a recent origin of the M. dilatata species complex or rate heterogeneity could be compromising phylogenetic inference. Rate heterogeneity detected in the mitochondrial data set seems to have no significant impacts on the phylogenies but clearly affects age estimates. Dating analyses show different estimations for the speciation of M. dilatata species complex depending on whether taking compositional heterogeneity into account (0.8 [0.05–2.6] Myr) or assuming rate homogeneity (0.4 [0.14–0.75] Myr). Genomic data also provided evidence of introgression among all analysed samples of the complex. RADseq data indicated that M. capitata colour morphs may have a genetic basis. Conclusions Despite the volume of data (over 60,000 SNPs), phylogenetic relationships within the M. dilatata species complex remain unresolved most likely due to a recent origin and ongoing introgression. Species delimitation with genomic data is not concordant with the current taxonomy, which does not reflect the true diversity of this group. Nominal species within the complex are either undergoing a speciation process or represent ecomorphs exhibiting phenotypic polymorphisms.info:eu-repo/semantics/publishedVersio

Getting a grip at the edge: recolonization and introgression in eastern Pacific Porites corals

© 2016 John Wiley & Sons Ltd Aim: To infer species identity, population isolation, and geographical variation in inter-specific hybridization among corals of the genus Porites from the central and eastern tropical Pacific, with a focus on the timing of separation between populations of P. evermanni and P. lobata divided by the Eastern Pacific Barrier. Location: Hawaii, American Samoa, Panama and the Galapagos Islands of Ecuador. Methods: Maximum likelihood gene trees were obtained for mitochondrial DNA (COI), the internal transcribed spacer (ITS), and 5 single-copy nuclear (scn) gene regions. Allelic networks were used to group multi-locus scn data into species clusters despite some allele sharing. Coalescent analyses (IMa2) of the 5 scn markers were used to estimate the time of population divergence and test for introgression between P. evermanni and P. lobata. Results: Allelic networks based on scn gene sequences agreed with mtCOI and ITS designations. Divergence times between Hawaiian and eastern Pacific populations are consistent with an early Pleistocene recolonization of the eastern Pacific by P. evermanni followed by a more recent arrival of P. lobata. The two species were fully isolated in Hawaii/American Samoa populations, but introgression from P. evermanni into P. lobata was evident in the eastern Pacific. Main conclusions: These results are consistent with a scenario where a bout of introgression with P. evermanni, an early-arriving colonizer of the eastern Pacific suited to marginal environmental conditions, facilitated the later colonization of the more sensitive P. lobata

Using ezRAD to reconstruct the complete mitochondrial genome of Porites fontanesii (Cnidaria: Scleractinia)

Corals in the genus Porites are among the major framework builders of reef structures worldwide, yet the genus has been challenging to study due to a lack of informative molecular markers. Here, we used ezRAD sequencing to reconstruct the complete mitochondrial genome of Porites fontanesii (GenBank accession number MG754069), a widespread coral species endemic to the Red Sea and Gulf of Aden. The gene arrangement of P. fontanesii did not differ from other Scleractinia and consisted of 18,658 bp, organized in 13 protein-coding genes, 2 rRNA genes, and 2 tRNA genes. This mitochondrial genome contributes essential data to work towards a better understanding of evolutionary relationships within Porites

Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species

The Gila robusta species complex in the Lower Colorado River Basin has a complicated taxonomic history. Recent authors have separated this group into three nominal taxa, G. robusta, G. intermedia, and G. nigra, however aside from location, no reliable method of distinguishing individuals of these species currently exists. To assess relationships within this group, we examined morphology of type specimens and fresh material, and used RADseq methods to assess phylogenetic relationship among these nominal species. Maximum likelihood and Bayesian inference tree building methods reveal high concordance between tree topologies based on the mitochondrial and nuclear datasets. Coalescent SNAPP analysis resolved a similar tree topology. Neither morphological nor molecular data reveal diagnostic differences between these species as currently defined. As such, G. intermedia and G. nigra should be considered synonyms of the senior G. robusta. We hypothesize that climate driven wet and dry cycles have led to periodic isolation of population subunits and subsequent local divergence followed by reestablished connectivity and mixing. Management plans should therefore focus on retaining genetic variability and viability of geographic populations to preserve adaptability to changing climate conditions

Phylogenomics of Porites from the Arabian Peninsula

The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the scleractinian coral genus Porites. A total of 126 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 12 nominal and two unknown species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were compared and used to obtain thousands of genome-wide loci and SNPs. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus

Environmental latitudinal gradients and host specificity shape Symbiodiniaceae distribution in Red Sea Porites corals

AimTo assess the diversity of algal symbionts of the family Symbiodiniaceae associated with the coral genus Porites in the Red Sea, and to test for host-specificity and environmental variables driving biogeographical patterns of algal symbiont distribution.LocationSaudi Arabian Red SeaTaxonEndosymbiotic dinoflagellates of the family Symbiodiniaceae in association with the reef-building coral genus Porites.MethodsEighty Porites coral specimens were collected along the Saudi Arabian Red Sea coast. Species boundaries were assessed morphologically and genetically (putative Control Region - mtCR; ITS region – ITS). Community composition of symbiotic dinoflagellates of the family Symbiodiniaceae was also assessed. Using the ITS2 marker with the SymPortal framework, Symbiodiniaceae data at the genus, majority ITS2 sequence, and ITS2 type profile were used to assess symbiont diversity and distribution patterns. These were analyzed in relation to coral host diversity, geographic location, and environmental variables.ResultsAmong the 80 Porites samples, 10 morphologies were identified. These corals were clustered into five lineages (clades I to V) by each of the markers independently. Clades I, II, and III each comprised of a single Porites morphology, while clades IV and V contained up to five distinct morphologies. The diversity of Symbiodiniaceae associated with Porites was high and latitudinal differentiation was observed. In particular, a shift from a Cladocopium- to a Durusdinium-dominated community was found along the north-south gradient. Symbiont diversity showed patterns of geographic-specific association at Symbiodiniaceae genus, majority ITS2 sequence, and ITS2 type profile level. Specific associations with host-genotypes (but not morphological species) were also recovered when considering Symbiodiniaceae majority ITS2 sequence and ITS2 type profiles.Main conclusionsThis study provides the first large scale molecular characterization of Symbiodiniaceae communities associated with Porites corals from the Saudi Arabian Red Sea. The use of intragenomic diversity data enabled the resolution of host-symbiont specificity and biogeographical patterns of distribution, previously unachievable with the ITS2 marker alone. Finally, correlation among symbiont diversity and Red Sea environmental gradients was documented

Ecomorph or Endangered Coral? DNA and Microstructure Reveal Hawaiian Species Complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli

M. dilatata, M. flabellata, and M. patula and 80 other scleractinian corals were petitioned to be listed under the US Endangered Species Act (ESA), which would have major conservation implications. One of the difficulties with this evaluation is that reproductive boundaries between morphologically defined coral species are often permeable, and morphology can be wildly variable. We examined genetic and morphological variation in Hawaiian Montipora with a suite of molecular markers (mitochondrial: COI, CR, Cyt-B, 16S, ATP6; nuclear: ATPsβ, ITS) and microscopic skeletal measurements. Mitochondrial markers and the ITS region revealed four distinct clades: I) M. patula/M. verrilli, II) M. cf. incrassata, III) M. capitata, IV) M. dilatata/M. flabellata/M. cf. turgescens. These clades are likely to occur outside of Hawai'i according to mitochondrial control region haplotypes from previous studies. The ATPsβ intron data showed a pattern often interpreted as resulting from hybridization and introgression; however, incomplete lineage sorting may be more likely since the multicopy nuclear ITS region was consistent with the mitochondrial data. Furthermore, principal components analysis (PCA) of skeletal microstructure was concordant with the mitochondrial clades, while nominal taxa overlapped. The size and shape of verrucae or papillae contributed most to identifying groups, while colony-level morphology was highly variable. It is not yet clear if these species complexes represent population-level variation or incipient speciation (CA<1MYA), two alternatives that have very different conservation implications. This study highlights the difficulty in understanding the scale of genetic and morphological variation that corresponds to species as opposed to population-level variation, information that is essential for conservation and for understanding coral biodiversity

A simple molecular technique for distinguishing species reveals frequent misidentification of Hawaiian corals in the genus Pocillopora

Species within the scleractinian genus Pocillopora Lamarck 1816 exhibit extreme phenotypic plasticity, making identification based on morphology difficult. However, the mitochondrial open reading frame (mtORF) marker provides a useful genetic tool for identification of most species in this genus, with a notable exception of P. eydouxi and P. meandrina. Based on recent genomic work, we present a quick and simple, gel-based restriction fragment length polymorphism (RFLP) method for the identification of all six Pocillopora species occurring in Hawai‘i by amplifying either the mtORF region, a newly discovered histone region, or both, and then using the restriction enzymes targeting diagnostic sequences we unambiguously identify each species. Using this approach, we documented frequent misidentification of Pocillopora species based on colony morphology. We found that P. acuta colonies are frequently mistakenly identified as P. damicornis in Kāne‘ohe Bay, O‘ahu. We also found that P. meandrina likely has a northern range limit in the Northwest Hawaiian Islands, above which P. ligulata was regularly mistaken for P. meandrina